Genome-Wide Association Study and RNA Sequencing Identify Candidate Genes Regulating Nitrogen Use Efficiency and Associated Traits in Sorghum (Sorghum bicolor (L.) Moench)

    Bollam, S and Rayaprolu, L and Romana, K K and Ruperao, P and Selvanayagam, S and Vemula, A K and Adapala, G and Valluri, V K and Bajaj, P and Rathore, A and Odeny, D A and Srivastava, R K and Deshpande, S P and Gupta, R (2026) Genome-Wide Association Study and RNA Sequencing Identify Candidate Genes Regulating Nitrogen Use Efficiency and Associated Traits in Sorghum (Sorghum bicolor (L.) Moench). Food and Energy Security, 15 (1). pp. 1-37. ISSN 2048-3694

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    Abstract

    Sorghum (Sorghum bicolor L. Moench) is a resilient cereal crop with remarkable adaptability to diverse environments. Nitrogen use efficiency (NUE) is critical for improving sorghum yields, resource utilization, livelihood security, and environmental sustainability of the target ecologies. To dissect the physio-genetic variation of sorghum for NUE/Nitrogen (N) stress tolerance, a set of 186 diverse sorghum accessions was evaluated for 15 agro-physiological and NUE-related traits under three N regimes (0%, 50%, and 100% of the recommended [90 kg ha−1] dose) across two seasons. Genotyping-by-sequencing (GbS) SNP data enabled genome-wide association studies (GWAS). A total of 1369 marker-trait associations (MTAs) were detected across sorghum chromosomes, along with 69 candidate genes linked to N metabolism, including glutamine synthetase (GS), nitrate transporters, and sucrose-phosphate synthase. Transcriptome analysis of contrasting sorghum accessions detected 2229 (shoot) and 8661 (root) differentially expressed genes (DEGs). Integration of GWAS and transcriptomic data identified 10 key candidate genes such as the master N-regulators: the NIN-like protein (NLP), AP2/ERF transcription factor, ABC transporter, glutamine synthetase (GS), amino acid selective channel protein, F-box protein (FBP), SWEET transporter, glucose-1-phosphate adenylyltransferase (AGPase), and phosphofructokinase (PFK). Analysis of identified homologous gene groups across major cereals revealed evolutionary relationships and genetic conservation. Furthermore, this study identified contrasting sorghum accessions for N stress tolerance. The identified candidate genes and contrasting genetic stocks provide a foundation for the molecular dissection of NUE-related traits, offering clear targets for crop improvement via genomics-assisted breeding and gene editing technologies.

    Item Type: Article
    Divisions: Global Research Program - Accelerated Crop Improvement
    CRP: CGIAR Research Program on Grain Legumes and Dryland Cereals (GLDC)
    Uncontrolled Keywords: candidate gene, genome-wide association studies, genotypic variability, nitrogen use efficiency, sorghum, transcriptome analysis
    Subjects: Others > Genetic Engineering
    Mandate crops > Sorghum
    Others > Genetics and Genomics
    Depositing User: Mr Nagaraju T
    Date Deposited: 10 Feb 2026 05:20
    Last Modified: 10 Feb 2026 05:20
    URI: http://oar.icrisat.org/id/eprint/13471
    Official URL: https://onlinelibrary.wiley.com/doi/10.1002/fes3.7...
    Projects: CGIAR Research Program on Grain Legumes and Dryland Cereals
    Funders: Government of India - Department of Biotechnology, Biotechnology and Biological Sciences Research Council, Department of Science and Technology–National–Science and Engineering Research Board
    Acknowledgement: Funding support was provided by the Department of Biotechnology (DBT), Government of India, the Biotechnology and Biological Sciences Research Council (BBSRC), United Kingdom, for the CINTRIN-1 (BT/IN/UK-VNC/42/RG/2015-16 and BB/N013441/1) and CINTRIN-2 (BT/PR42631/AGIII/103/1312/2021) projects to Rajeev Gupta, Rakesh K. Srivastava, Santosh P. Deshpande, Abhishek Rathore, Laavanya Rayaprolu, Kirandeep Kaur Romana. The Department of Science and Technology–National Science and Engineering Research Board (DST-SERB) (PDF/2016/003203) provided support for the National Post-Doctoral Fellowship (NPDF) to Srikanth Bollam. This work was published as part of the CGIAR Research Program on Grain Legumes and Dryland Cereals (CRP-GLDC).
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